Nitrogen contamination in the southern half of Minnesota is so severe that 27 percent of the state’s lakes and rivers could not be used as drinking water, according to a new and unexpectedly blunt assessment of the state’s most prevalent form of water pollution.

The Minnesota Pollution Control Agency (MPCA) said Wednesday that, overall, 41 percent of Minnesota’s streams and lakes have excessive nitrogen, all of them in the state’s southern and central regions. The nutrient, which is used as fertilizer in agriculture and comes from wastewater treatment plants, can be toxic to fish and other forms of aquatic life. It is a primary cause of the vast oxygen-depleted area in the Gulf of Mexico known as the dead zone.

Even ambitious efforts could reduce nitrogen runoff by less than a third — and that would cost hundreds of millions of dollars, primarily in the agricultural regions of the state that contribute 70 percent of the total load, according to the MPCA’s report.

The scope of the problem and the cost of fixing it are so daunting that state Agriculture Commissioner Dave Frederickson said he questions whether it would be possible to achieve any significant reduction.

“Maybe we are chasing our tail,” he said after MPCA Commissioner John Linc Stine finished presenting the findings at a news conference Wednesday. “Maybe we will never get there.”

But environmentalists, who have long been critical of state regulators’ reluctance to tackle the nitrogen problem, said they were surprised and pleased at the candor and the depth of the analysis. Several said they expect it will inspire a debate about the fundamental problem — the agriculture industry’s reliance on just two crops — corn and soybeans, both of which are primary drivers of the pollutant.

Current plans to attack the problem by persuading farmers to adopt expensive and not very effective methods to control nitrogen are just “lipstick on a pig,” said Trevor Russell, watershed program director for Friends of the Mississippi River. “At some point we have to change the pig.”

Farm groups say farmers have already made significant progress in managing the use of fertilizer and manure. Over time, fertilizer use has declined sharply and has become much more precise. New methods to clean nitrogen from surface runoff and drainage systems below row crops are increasingly being adopted, said Adam Birr, research director for the Minnesota Corn Growers Association.

“We are not starting from scratch,” Birr said. And Stine said that while nitrogen levels in many rivers — including the Mississippi — have been rising for years, in some places in the heart of the state’s agricultural region they have declined or leveled off.

Dangers to residents

The 400-page analysis is the most comprehensive the state has ever conducted for nitrogen. It will provide some of the baseline information needed for an upcoming statewide water quality standard used to protect wildlife and aquatic ecosystems from the effects of nitrogen. Separately, the federal government has a long-established nitrogen standard for drinking water, 10 parts per million, designed to protect infants from a sometimes lethal condition known as blue baby syndrome.

The MPCA, along with scientists from the University of Minnesota and other state and federal agencies, examined 50,000 water samples from 75 watersheds, and tracked concentrations in multiple sites over several decades.

They found that 27 percent of the surface waters exceeded the federal drinking-water standard, and 41 percent had concentrations of 5 parts per million or more.

Nitrogen concentrations in the Mississippi are modest in the river’s upper reaches, where there is little agriculture. Nonetheless, the river showed increasing concentrations between 1976 and 2010 — increases ranging from 87 to 268 percent — everywhere between Camp Ripley and La Crosse. In more recent years, nitrate concentrations were increasing everywhere downstream of Clearwater at a rate of 1 to 4 percent per year.

Pollution source

In a new finding, pollution officials said 30 percent of the nitrogen in lakes and rivers comes from contaminated groundwater. In Minnesota, where groundwater supplies most people with drinking water, about 6 percent of wells are contaminated with nitrogen. Some cities spend tens of millions to install systems to remove nitrogen from drinking water.

By far, the major source of nitrogen was agriculture; nearly 70 percent came from cropland groundwater and from tile drainage systems. Wastewater treatment plants supplied 9 percent, while urban and cropland surface runoff contributed 6 percent, with the rest coming from air, forests and other minor sources.

If every farmer in the state did as much a possible to reduce nitrogen losses — planting marginal land with grasses, running tainted water through wetlands or wood chips to remove nitrogen, planting cover crops between harvests, and applying fertilizer only in the spring — the state could reduce the pollution by 30 percent.

Some questioned whether that’s enough.

Deborah Swackhamer, co-director of the Minnesota Water Resources Center at the U, said the goal established by a federal task force to fix the Gulf of Mexico dead zone is a 45 percent reduction of nitrogen in the Mississippi watershed.

“If it’s proportional, Minnesota needs to reduce its load by 45 percent,” she said. And that doesn’t address the state’s drinking water problem, which she said is far more important.

A 30 percent reduction would cost $22 to $47 million per watershed per year.

Investing in health

Still, Stine and others said innovation may yet solve the problem. Four watersheds in Minnesota are participating in a $9.5 million project to find out if farmers can voluntarily adopt proven practices to protect water quality. Birr, of the corn growers association, said the group has helped fund two positions at the university to provide agricultural research and education for farmers.

That’s because corn and soybeans will be the crop of choice for most farmers as long as that’s what the markets dictate, Frederickson said.

“It’s all ag economics,” he said. “Farmers are doing the best they can. “